{"id":"https://openalex.org/W2103873225","doi":"https://doi.org/10.1093/nar/gkl039","title":"UMMS: constrained harmonic and anharmonic analyses of macromolecules based on elastic network models","display_name":"UMMS: constrained harmonic and anharmonic analyses of macromolecules based on elastic network models","publication_year":2006,"publication_date":"2006-07-01","ids":{"openalex":"https://openalex.org/W2103873225","doi":"https://doi.org/10.1093/nar/gkl039","mag":"2103873225","pmid":"https://pubmed.ncbi.nlm.nih.gov/16845072"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkl039","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkl039","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_2/W57/7622608/gkl039.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/34/suppl_2/W57/7622608/gkl039.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5111294654","display_name":"Yoonna Jang","orcid":null},"institutions":[{"id":"https://openalex.org/I24603500","display_name":"University of Massachusetts Amherst","ror":"https://ror.org/0072zz521","country_code":"US","type":"education","lineage":["https://openalex.org/I24603500"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Y. Jang","raw_affiliation_strings":["Department of Mechanical and Industrial Engineering, University of Massachusetts, Amherst, MA 01003, USA","Department of Mechanical and Industrial Engineering, University of Massachusetts, Amherst, MA 01003 USA"],"affiliations":[{"raw_affiliation_string":"Department of Mechanical and Industrial Engineering, University of Massachusetts, Amherst, MA 01003, USA","institution_ids":["https://openalex.org/I24603500"]},{"raw_affiliation_string":"Department of Mechanical and Industrial Engineering, University of Massachusetts, Amherst, MA 01003 USA","institution_ids":["https://openalex.org/I24603500"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005778140","display_name":"Jaepil Jeong","orcid":"https://orcid.org/0000-0002-1453-0964"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"J. I. Jeong","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5084320255","display_name":"Moon Kyu Kim","orcid":"https://orcid.org/0000-0001-6186-3991"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"M. K. Kim","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5111294654"],"corresponding_institution_ids":["https://openalex.org/I24603500"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":1.0597,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.74829739,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"34","issue":"Web Server","first_page":"W57","last_page":"W62"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9965999722480774,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/anharmonicity","display_name":"Anharmonicity","score":0.9256566762924194},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.6755275726318359},{"id":"https://openalex.org/keywords/macromolecule","display_name":"Macromolecule","score":0.6348515748977661},{"id":"https://openalex.org/keywords/interpolation","display_name":"Interpolation (computer graphics)","score":0.6013672351837158},{"id":"https://openalex.org/keywords/harmonic","display_name":"Harmonic","score":0.5707507729530334},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.5071277618408203},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.48286134004592896},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.46992361545562744},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.4495406150817871},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.34824395179748535},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.33093202114105225},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.31134670972824097},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.2865099012851715},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.1784692406654358},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.1518823206424713},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.14764663577079773},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09538933634757996}],"concepts":[{"id":"https://openalex.org/C147724859","wikidata":"https://www.wikidata.org/wiki/Q545228","display_name":"Anharmonicity","level":2,"score":0.9256566762924194},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.6755275726318359},{"id":"https://openalex.org/C204389451","wikidata":"https://www.wikidata.org/wiki/Q178593","display_name":"Macromolecule","level":2,"score":0.6348515748977661},{"id":"https://openalex.org/C137800194","wikidata":"https://www.wikidata.org/wiki/Q11713455","display_name":"Interpolation (computer graphics)","level":3,"score":0.6013672351837158},{"id":"https://openalex.org/C127934551","wikidata":"https://www.wikidata.org/wiki/Q1148098","display_name":"Harmonic","level":2,"score":0.5707507729530334},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.5071277618408203},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.48286134004592896},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.46992361545562744},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.4495406150817871},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.34824395179748535},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.33093202114105225},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.31134670972824097},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2865099012851715},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.1784692406654358},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.1518823206424713},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.14764663577079773},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09538933634757996},{"id":"https://openalex.org/C104114177","wikidata":"https://www.wikidata.org/wiki/Q79782","display_name":"Motion (physics)","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D004548","descriptor_name":"Elasticity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004548","descriptor_name":"Elasticity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004548","descriptor_name":"Elasticity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009038","descriptor_name":"Motion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009038","descriptor_name":"Motion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009038","descriptor_name":"Motion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D046911","descriptor_name":"Macromolecular Substances","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D046911","descriptor_name":"Macromolecular Substances","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D046911","descriptor_name":"Macromolecular Substances","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gkl039","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkl039","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_2/W57/7622608/gkl039.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:16845072","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16845072","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:1538792","is_oa":true,"landing_page_url":"http://doi.org/10.1093/nar/gkl039","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkl039","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkl039","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_2/W57/7622608/gkl039.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7","score":0.6800000071525574}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2103873225.pdf","grobid_xml":"https://content.openalex.org/works/W2103873225.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W1247114292","https://openalex.org/W1981099976","https://openalex.org/W1986966735","https://openalex.org/W1991762941","https://openalex.org/W2001449162","https://openalex.org/W2011890903","https://openalex.org/W2026258231","https://openalex.org/W2031340110","https://openalex.org/W2033906450","https://openalex.org/W2062809320","https://openalex.org/W2069777230","https://openalex.org/W2071152222","https://openalex.org/W2072575434","https://openalex.org/W2082462938","https://openalex.org/W2088906583","https://openalex.org/W2101017457","https://openalex.org/W2102211745","https://openalex.org/W2105254477","https://openalex.org/W2106988671","https://openalex.org/W2112315506","https://openalex.org/W2113554569","https://openalex.org/W2113994268","https://openalex.org/W2130479394","https://openalex.org/W2142960527","https://openalex.org/W2145961753","https://openalex.org/W2146249023","https://openalex.org/W2146770788","https://openalex.org/W2148455468"],"related_works":["https://openalex.org/W2963075460","https://openalex.org/W2510396871","https://openalex.org/W2161357890","https://openalex.org/W2610572818","https://openalex.org/W4389355097","https://openalex.org/W4224874860","https://openalex.org/W2032446402","https://openalex.org/W2992233353","https://openalex.org/W4293162175","https://openalex.org/W2082550390"],"abstract_inverted_index":{"UMass":[0],"Morph":[1],"Server":[2],"(UMMS)":[3],"has":[4,27],"been":[5,28,94],"developed":[6,95],"for":[7,34],"the":[8,12,86],"broad":[9],"impact":[10],"on":[11],"study":[13],"of":[14,23,84,108,119],"molecular":[15],"dynamics":[16],"(MD).":[17],"The":[18],"elastic":[19,124],"network":[20,125],"model":[21],"(ENM)":[22],"a":[24,31,72,75,109,120],"given":[25],"macromolecule":[26,111],"proven":[29],"as":[30],"useful":[32],"tool":[33],"analyzing":[35],"thermal":[36],"behaviors":[37],"locally":[38],"and":[39,81,90,96,112],"predicting":[40],"folding":[41],"pathways":[42],"globally.":[43],"UMMS":[44],"utilizes":[45],"coarse-grained":[46],"ENMs":[47,92],"at":[48,98,127],"various":[49],"levels.":[50],"These":[51],"simplifications":[52],"remarkably":[53],"save":[54],"computation":[55],"time":[56],"compared":[57],"with":[58],"all-atom":[59],"MD":[60],"simulations":[61],"so":[62],"that":[63],"one":[64],"can":[65,101],"bring":[66],"down":[67],"massive":[68],"computational":[69,79],"problems":[70],"from":[71],"supercomputer":[73],"to":[74],"PC.":[76],"To":[77],"improve":[78],"efficiency":[80],"physical":[82],"reality":[83],"ENMs,":[85],"symmetry-constrained,":[87],"rigid-cluster,":[88],"hybrid":[89],"chemical-bond":[91],"have":[93],"implemented":[97],"UMMS.":[99],"One":[100],"request":[102],"both":[103],"harmonic":[104],"normal":[105],"mode":[106],"analysis":[107],"single":[110],"anharmonic":[113],"pathway":[114],"generation":[115],"between":[116],"two":[117],"conformations":[118],"same":[121],"molecule":[122],"using":[123],"interpolation":[126],"http://biomechanics.ecs.umass.edu/umms.html.":[128]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
